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Hi experts, 

I have previously analysed my EPI resting-state data with the following pipeline using command line tools, but I would like to add distortion correction and I am unsure at what stage to perform slice timer, motion correction (mcflirt), and distortion correction. 

Old pipeline:
  1. STRUCTURAL PREPROCESSING (Input is T1 image)
    1. fslreorient2std 
    2. BET brain extraction on T1's
    3. FLIRT (register T1 to standard space and generate and affine)
    4. FNIRT (coregister T1 native to standard space)
  2. FUNCTIONAL PREPROCESSING (input is resting-state EPI)
    1. fslreorient2std
    2. slicetimer
    3. mcflirt
    4. fslmaths -Tmean to get a merged and average .nii using the mean across time
  3. functional FLIRT (-in = is fslmaths'd output, -ref = bet'd T1)
  4. applywarp based on native T1 (--in= mcflirt'd functional --premat = affine from flirt)

My question is, at what stage in the above pipeline could I perform distortion correction? Below are my steps to perform distortion correcton which works well. However, I would like to also perform slice timer and motion correction so I have attempted to input the mcflirt'd output into epi_reg but that does not work. 
  1. fsl_prepare_fieldmap
  2. epi_reg: epi_reg --epi=ep2d_3_3iso_Resting.nii --t1=t1.nii.gz --t1brain=bet_brain.nii.gz --fmap=fieldmap.nii.gz --fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_BET.nii.gz --echospacing=0.00035 --pedir=-y --out=epi2struc
  3. structural flirt: flirt -in myStructuralImage -ref myStandardSpaceImage -omat struct2standard.mat
  4. functional flirt:  flirt -in epi2struc.nii.gz -ref myStandardSpaceImage -out epi2standard -applyxfm -init struct2standard.mat
Any help is greatly appreciated. Thank you!

Kind regards,
Sally.